Observation of trends in physical education plays an integral role in motor-development diagnostics and in encouraging physical activity and a healthy lifestyle. This study aims to elucidate the current state of and trends in pupils' assessments of physical education lessons (PELs) in different education systems in the context of self-perception of physical fitness. The research was conducted during PELs taught by student teachers at primary schools and high schools in the Czech Republic and in Poland. Schools were selected annually between 2000 and 2011 according to the student teachers' places of residence. In total, the research involved 25,988 Czech pupils and 21,205 Polish pupils. At the end of each PEL, an anonymous questionnaire was distributed. The Czech and Polish versions contained cognitive, emotional, health, social, attitudinal, and creative dimensions and the supplementary dimension "pupil's role". For the analysis, pupils were divided according to their self-perceived physical fitness (SPF) as marked in the questionnaire (low or high). Polish and Czech pupils who evaluated themselves as having high physical fitness gave PELs higher evaluations, both overall and in individual dimensions, than those who evaluated themselves as having low physical fitness. During three 4-year periods between 2000 and 2011, a decline in positive PEL evaluations occurred in all groups, except among Polish girls with low SPF. A low positive-assessment rate was found in Czech girls with low SPF. The lowest rate was found in Czech boys with low SPF. The Polish system of education includes more weekly PEL and offers vocational training for PE teachers, facilitating more positive evaluation of PEL by pupils compared with the Czech system. It is necessary to focus on meeting the needs of pupils with low SPF during teacher training and in teaching.